In the past, match worn shirts would have a different spec to the ones on sale to the general public. This probably only happens at the big clubs now, although I am not party to how Genesis Sports/Provan produce our first team tops.
You mentioned that our sponsor is embossed, I hadn't realised this. The last embossed sponsors logo that I can remember was on the Pony Motorola shirts (see pic). In saying that, I don't buy shirts so there may have been others. Usually these days the sponsors logo is either printed on or heat transferred.
I have to admit that I do favour a properly embroidered badge, however the players comfort comes first, and if nipple rash is an issue the badge should be printed on to the shirt, not stitched.
The kit contract is up at the end of the season and we will just need to wait to see if Genesis sign up for a few more years. However if what you say is correct, these niggling problems may force the kit man and Provan to seek pastures new.